Over 50 single nucleotide polymorphisms (SNPs) have been identified by genome wide association studies (GWAS) to be associated with susceptibility to type 2 diabetes (T2D); however the causal gene in most cases is not known. In this study we sought to identify which may be the most likely causal genes at five T2D GWAS loci by measuring their expression in control and T2D islets, as well as observing their regulation by glucose. We measured the expression of ten genes at five loci (CDKN2A/2B, CDC123/CAMK-1D, HHEX/IDE, TSPAN8/LGR5, and DGKB/TMEM 195), in control and human pancreatic islets by real-time PCR. We then measured the expression of these genes in the rodent pancreatic beta cell line INS-1 exposed to 5.6 mmol/l, 11 mmol/l and 28 mmol/l glucose for 48 hours. We found differential expression of the longest isoform of CDKN2B specifically between control and T2D human islets, whereas the shortest isoform of this gene had no expression in islets. Tmem195 was the only gene to show differential expression in response to increasing glycemia in INS-1 cells under the conditions described. Our study is an example of how the differential expression of genes in loci spanning more than one gene can aid identification of the more likely causal gene.